{"id":"https://openalex.org/W2070853446","doi":"https://doi.org/10.1074/jbc.m112.388538","title":"Structural Basis of Biological Nitrile Reduction","display_name":"Structural Basis of Biological Nitrile Reduction","publication_year":2012,"publication_date":"2012-07-12","ids":{"openalex":"https://openalex.org/W2070853446","doi":"https://doi.org/10.1074/jbc.m112.388538","mag":"2070853446","pmid":"https://pubmed.ncbi.nlm.nih.gov/22787148","pmcid":"https://www.ncbi.nlm.nih.gov/pmc/articles/3436371"},"language":"en","primary_location":{"id":"doi:10.1074/jbc.m112.388538","doi":"https://doi.org/10.1074/jbc.m112.388538","is_oa":true,"landing_page_url":"https://doi.org/10.1074/jbc.m112.388538","pdf_url":null,"source":{"id":"https://openalex.org/S140251998","display_name":"Journal of Biological Chemistry","issn_l":"0021-9258","issn":["0021-9258","1067-8816","1083-351X"],"is_oa":false,"is_in_doaj":true,"is_core":true,"listed_in":["anvur-scientific","cwts-core","doaj","dongbi-b","doyens","jufo-2","ki-jl-2","medline","norway-2","poland-100","vabb-shw"],"host_organization":"https://openalex.org/P4310320990","host_organization_name":"Elsevier BV","host_organization_lineage":["https://openalex.org/P4310320990"],"host_organization_lineage_names":["Elsevier BV"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Biological Chemistry","raw_type":"journal-article"},"volume":null,"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"hybrid","oa_url":"https://doi.org/10.1074/jbc.m112.388538","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5050488251","display_name":"Vimbai M. Chikwana","orcid":null,"observed_orcids":[]},"institutions":[{"id":"https://openalex.org/I126345244","display_name":"Portland State University","ror":"https://ror.org/00yn2fy02","country_code":"US","type":"education","lineage":["https://openalex.org/I126345244"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Vimbai M. Chikwana","raw_affiliation_strings":["Department of Chemistry, Portland State University, Portland, OR 97207, USA","Department of Chemistry, Portland State University, Portland, Oregon 97207"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Chemistry, Portland State University, Portland, OR 97207, USA","institution_ids":["https://openalex.org/I126345244"]},{"raw_affiliation_string":"Department of Chemistry, Portland State University, Portland, Oregon 97207","institution_ids":["https://openalex.org/I126345244"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5084942532","display_name":"Boguslaw Stec","orcid":"https://orcid.org/0000-0002-8696-0349","observed_orcids":["https://orcid.org/0000-0002-8696-0349"]},"institutions":[{"id":"https://openalex.org/I188891513","display_name":"Sanford Burnham Prebys Medical Discovery Institute","ror":"https://ror.org/03m1g2s55","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I188891513"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Boguslaw Stec","raw_affiliation_strings":["Sanford-Burnham Medical Research Institute, La Jolla, California 92037"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Sanford-Burnham Medical Research Institute, La Jolla, California 92037","institution_ids":["https://openalex.org/I188891513"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5021388884","display_name":"Bobby W.K. Lee","orcid":null,"observed_orcids":[]},"institutions":[{"id":"https://openalex.org/I126345244","display_name":"Portland State University","ror":"https://ror.org/00yn2fy02","country_code":"US","type":"education","lineage":["https://openalex.org/I126345244"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Bobby W.K. Lee","raw_affiliation_strings":["Department of Chemistry, Portland State University, Portland, Oregon 97207"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Chemistry, Portland State University, Portland, Oregon 97207","institution_ids":["https://openalex.org/I126345244"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5013938980","display_name":"Val\u00e9rie de Cr\u00e9cy\u2010Lagard","orcid":"https://orcid.org/0000-0002-9955-3785","observed_orcids":["https://orcid.org/0000-0002-9955-3785"]},"institutions":[{"id":"https://openalex.org/I33213144","display_name":"University of Florida","ror":"https://ror.org/02y3ad647","country_code":"US","type":"education","lineage":["https://openalex.org/I33213144"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Val\u00e9rie de Cr\u00e9cy-Lagard","raw_affiliation_strings":["Department of Microbiology and Cell Science, University of Florida, Gainesville, Florida 32611-0700"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Microbiology and Cell Science, University of Florida, Gainesville, Florida 32611-0700","institution_ids":["https://openalex.org/I33213144"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5080737135","display_name":"Dirk Iwata\u2010Reuyl","orcid":"https://orcid.org/0000-0001-9456-3864","observed_orcids":["https://orcid.org/0000-0001-9456-3864"]},"institutions":[{"id":"https://openalex.org/I126345244","display_name":"Portland State University","ror":"https://ror.org/00yn2fy02","country_code":"US","type":"education","lineage":["https://openalex.org/I126345244"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Dirk Iwata-Reuyl","raw_affiliation_strings":["Department of Chemistry, Portland State University, Portland, Oregon 97207"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Chemistry, Portland State University, Portland, Oregon 97207","institution_ids":["https://openalex.org/I126345244"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5038859577","display_name":"Manal A. Swairjo","orcid":"https://orcid.org/0000-0003-1334-1763","observed_orcids":["https://orcid.org/0000-0003-1334-1763"]},"institutions":[{"id":"https://openalex.org/I93393672","display_name":"Western University of Health Sciences","ror":"https://ror.org/05167c961","country_code":"US","type":"education","lineage":["https://openalex.org/I93393672"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Manal A. Swairjo","raw_affiliation_strings":["Graduate College of Biomedical Sciences, Western University of Health Sciences, Pomona, California 91766-1854"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Graduate College of Biomedical Sciences, Western University of Health Sciences, Pomona, California 91766-1854","institution_ids":["https://openalex.org/I93393672"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5038859577","https://openalex.org/A5080737135"],"corresponding_institution_ids":["https://openalex.org/I126345244","https://openalex.org/I93393672"],"apc_list":{"value":3430,"currency":"USD","value_usd":3430},"apc_paid":{"value":3430,"currency":"USD","value_usd":3430},"fwci":1.1759,"has_fulltext":false,"cited_by_count":32,"citation_normalized_percentile":{"value":0.76773315,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":99},"biblio":{"volume":"287","issue":"36","first_page":"30560","last_page":"30570"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11162","display_name":"Enzyme Structure and Function","score":0.9653000235557556,"subfield":{"id":"https://openalex.org/subfields/2505","display_name":"Materials Chemistry"},"field":{"id":"https://openalex.org/fields/25","display_name":"Materials Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},"topics":[{"id":"https://openalex.org/T11162","display_name":"Enzyme Structure and Function","score":0.9653000235557556,"subfield":{"id":"https://openalex.org/subfields/2505","display_name":"Materials Chemistry"},"field":{"id":"https://openalex.org/fields/25","display_name":"Materials Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T12827","display_name":"Biochemical and Molecular Research","score":0.014600000344216824,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T10044","display_name":"Protein Structure and Dynamics","score":0.008299999870359898,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/nitrile-reduction","display_name":"nitrile reduction","score":0.9620000123977661},{"id":"https://openalex.org/keywords/bacillus-subtilis","display_name":"Bacillus subtilis","score":0.9300000071525574},{"id":"https://openalex.org/keywords/enzyme-crystal-structure","display_name":"enzyme crystal structure","score":0.6539999842643738},{"id":"https://openalex.org/keywords/hydride-transfer","display_name":"hydride transfer","score":0.8420000076293945},{"id":"https://openalex.org/keywords/conformational-change","display_name":"conformational change","score":0.8560000061988831},{"id":"https://openalex.org/keywords/enzyme-mechanism","display_name":"enzyme mechanism","score":0.35899999737739563}],"concepts":[{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.7690869569778442},{"id":"https://openalex.org/C2779240715","wikidata":"https://www.wikidata.org/wiki/Q333936","display_name":"Nitrile","level":2,"score":0.7271770238876343},{"id":"https://openalex.org/C41183919","wikidata":"https://www.wikidata.org/wiki/Q423026","display_name":"Active site","level":3,"score":0.7043517827987671},{"id":"https://openalex.org/C71240020","wikidata":"https://www.wikidata.org/wiki/Q186011","display_name":"Stereochemistry","level":1,"score":0.6180832386016846},{"id":"https://openalex.org/C180577832","wikidata":"https://www.wikidata.org/wiki/Q127920","display_name":"Covalent bond","level":2,"score":0.551215648651123},{"id":"https://openalex.org/C2777289219","wikidata":"https://www.wikidata.org/wiki/Q7632154","display_name":"Substrate (aquarium)","level":2,"score":0.4183838367462158},{"id":"https://openalex.org/C181199279","wikidata":"https://www.wikidata.org/wiki/Q8047","display_name":"Enzyme","level":2,"score":0.3422726094722748},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.14468050003051758},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.08864089846611023},{"id":"https://openalex.org/C178790620","wikidata":"https://www.wikidata.org/wiki/Q11351","display_name":"Organic chemistry","level":1,"score":0.06631463766098022},{"id":"https://openalex.org/C18903297","wikidata":"https://www.wikidata.org/wiki/Q7150","display_name":"Ecology","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D001412","descriptor_name":"Bacillus subtilis","qualifier_ui":"Q000201","qualifier_name":"enzymology","is_major_topic":true},{"descriptor_ui":"D001412","descriptor_name":"Bacillus subtilis","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D001426","descriptor_name":"Bacterial Proteins","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D001426","descriptor_name":"Bacterial Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D001426","descriptor_name":"Bacterial Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D009570","descriptor_name":"Nitriles","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D009570","descriptor_name":"Nitriles","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D010084","descriptor_name":"Oxidation-Reduction","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D010088","descriptor_name":"Oxidoreductases","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D010088","descriptor_name":"Oxidoreductases","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D010088","descriptor_name":"Oxidoreductases","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D019943","descriptor_name":"Amino Acid Substitution","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020125","descriptor_name":"Mutation, Missense","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":4,"locations":[{"id":"doi:10.1074/jbc.m112.388538","doi":"https://doi.org/10.1074/jbc.m112.388538","is_oa":true,"landing_page_url":"https://doi.org/10.1074/jbc.m112.388538","pdf_url":null,"source":{"id":"https://openalex.org/S140251998","display_name":"Journal of Biological Chemistry","issn_l":"0021-9258","issn":["0021-9258","1067-8816","1083-351X"],"is_oa":false,"is_in_doaj":true,"is_core":true,"listed_in":["anvur-scientific","cwts-core","doaj","dongbi-b","doyens","jufo-2","ki-jl-2","medline","norway-2","poland-100","vabb-shw"],"host_organization":"https://openalex.org/P4310320990","host_organization_name":"Elsevier BV","host_organization_lineage":["https://openalex.org/P4310320990"],"host_organization_lineage_names":["Elsevier BV"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Biological Chemistry","raw_type":"journal-article"},{"id":"pmh:oai:europepmc.org:2747142","doi":null,"is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/3436371","pdf_url":null,"source":{"id":"https://openalex.org/S4306400806","display_name":"Europe PMC (PubMed Central)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I1303153112","host_organization_name":"European Bioinformatics Institute","host_organization_lineage":["https://openalex.org/I1303153112"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":null,"raw_type":"Text"},{"id":"pmh:oai:pubmedcentral.nih.gov:3436371","doi":null,"is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/3436371","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"J Biol Chem","raw_type":"Text"},{"id":"pmid:22787148","doi":null,"is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/22787148","pdf_url":null,"source":{"id":"https://openalex.org/S4306525036","display_name":"PubMed","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"The Journal of biological chemistry","raw_type":"Journal Article"}],"best_oa_location":{"id":"doi:10.1074/jbc.m112.388538","doi":"https://doi.org/10.1074/jbc.m112.388538","is_oa":true,"landing_page_url":"https://doi.org/10.1074/jbc.m112.388538","pdf_url":null,"source":{"id":"https://openalex.org/S140251998","display_name":"Journal of Biological Chemistry","issn_l":"0021-9258","issn":["0021-9258","1067-8816","1083-351X"],"is_oa":false,"is_in_doaj":true,"is_core":true,"listed_in":["anvur-scientific","cwts-core","doaj","dongbi-b","doyens","jufo-2","ki-jl-2","medline","norway-2","poland-100","vabb-shw"],"host_organization":"https://openalex.org/P4310320990","host_organization_name":"Elsevier BV","host_organization_lineage":["https://openalex.org/P4310320990"],"host_organization_lineage_names":["Elsevier BV"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Biological Chemistry","raw_type":"journal-article"},"sustainable_development_goals":[],"study_designs":[],"awards":[{"id":"https://openalex.org/G102211516","display_name":"Synthesis and function of Queuosine in Bacteria","funder_award_id":"R01GM070641","funder_id":"https://openalex.org/F4320337354","funder_display_name":"National Institute of General Medical Sciences"},{"id":"https://openalex.org/G6276651706","display_name":null,"funder_award_id":"GM70641","funder_id":"https://openalex.org/F4320337354","funder_display_name":"National Institute of General Medical Sciences"}],"funders":[{"id":"https://openalex.org/F4320337354","display_name":"National Institute of General Medical Sciences","ror":"https://ror.org/04q48ey07"}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":24,"referenced_works":["https://openalex.org/W1520730837","https://openalex.org/W1539796472","https://openalex.org/W1553518074","https://openalex.org/W1964087678","https://openalex.org/W1994342014","https://openalex.org/W1996454766","https://openalex.org/W2001127189","https://openalex.org/W2010355629","https://openalex.org/W2014504234","https://openalex.org/W2016765195","https://openalex.org/W2033735656","https://openalex.org/W2038840577","https://openalex.org/W2046790499","https://openalex.org/W2048245383","https://openalex.org/W2059158458","https://openalex.org/W2118752014","https://openalex.org/W2121400034","https://openalex.org/W2122327402","https://openalex.org/W2142055302","https://openalex.org/W2144081223","https://openalex.org/W2466464310","https://openalex.org/W2786774014","https://openalex.org/W2886382167","https://openalex.org/W6601532982"],"related_works":["https://openalex.org/W1584292606","https://openalex.org/W2059158458","https://openalex.org/W2533088637","https://openalex.org/W2783673228","https://openalex.org/W2142055302","https://openalex.org/W2121400034","https://openalex.org/W2164165967","https://openalex.org/W3170146235","https://openalex.org/W4309422994","https://openalex.org/W2010355629"],"abstract_inverted_index":{"The":[0,71],"enzyme":[1,38,73],"QueF":[2,72],"catalyzes":[3],"the":[4,7,16,36,42,54,57,60,66,90,106,116,142,154,157],"reduction":[5,19],"of":[6,10,30,35,59,79,141,156],"nitrile":[8,18],"group":[9],"7-cyano-7-deazaguanine":[11],"(preQ(0))":[12],"to":[13,115],"7-aminomethyl-7-deazaguanine":[14],"(preQ(1)),":[15],"only":[17],"reaction":[20],"known":[21],"in":[22,39,53,63,105,138],"biology.":[23],"We":[24],"describe":[25],"here":[26],"two":[27,80],"crystal":[28],"structures":[29],"Bacillus":[31],"subtilis":[32],"QueF,":[33],"one":[34],"wild-type":[37,107],"complex":[40,64],"with":[41,65],"substrate":[43,67],"preQ(0),":[44],"trapped":[45],"as":[46],"a":[47,50,96,111,134,151],"covalent":[48,113],"thioimide,":[49],"putative":[51],"intermediate":[52],"reaction,":[55],"and":[56,104,122,139,160],"second":[58],"C55A":[61],"mutant":[62],"preQ(0)":[68,97,128],"bound":[69,100],"noncovalently.":[70],"forms":[74,110],"an":[75],"asymmetric":[76],"tunnel-fold":[77],"homodecamer":[78],"head-to-head":[81],"facing":[82],"pentameric":[83],"subunits,":[84],"harboring":[85],"10":[86],"active":[87,143],"sites":[88],"at":[89,101],"intersubunit":[91],"interfaces.":[92],"In":[93],"both":[94],"structures,":[95],"molecule":[98],"is":[99],"eight":[102],"sites,":[103],"enzyme,":[108],"it":[109],"thioimide":[112,131],"linkage":[114],"catalytic":[117],"residue":[118],"Cys-55.":[119],"Both":[120],"structural":[121],"transient":[123],"kinetic":[124],"data":[125],"show":[126],"that":[127],"binding,":[129],"not":[130],"formation,":[132],"induces":[133],"large":[135],"conformational":[136],"change":[137],"closure":[140],"site.":[144],"Based":[145],"on":[146],"these":[147],"data,":[148],"we":[149],"propose":[150],"mechanism":[152],"for":[153],"activation":[155],"Cys-55":[158],"nucleophile":[159],"subsequent":[161],"hydride":[162],"transfer.":[163]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2024,"cited_by_count":2},{"year":2023,"cited_by_count":1},{"year":2021,"cited_by_count":2},{"year":2019,"cited_by_count":2},{"year":2018,"cited_by_count":5},{"year":2017,"cited_by_count":4},{"year":2016,"cited_by_count":6},{"year":2015,"cited_by_count":2},{"year":2014,"cited_by_count":2},{"year":2013,"cited_by_count":2},{"year":2012,"cited_by_count":2}],"updated_date":"2026-10-31T12:09:11.096373","created_date":"2016-06-24T00:00:00"}
